Metagenomic species profiling using universal phylogenetic marker genes

Shinichi Sunagawa; Daniel R. Mende; Georg Zeller; Fernando Izquierdo-Carrasco; Simon A. Berger; Jens Roat Kultima; Luis Pedro Coelho; Manimozhiyan Arumugam; Julien Tap; Henrik Bjørn Nielsen; Simon Rasmussen; Søren Brunak; Oluf Borbye Pedersen; Francisco Guarner; Willem M de Vos; Jun Wang; Junhua Li; Joël Doré; S Dusko Ehrlich; Alexandros Stamatakis; Peer Bork

doi:10.1038/nmeth.2693

Metagenomic species profiling using universal phylogenetic marker genes

Shinichi Sunagawa, Daniel R. Mende, Georg Zeller, Fernando Izquierdo-Carrasco, Simon A. Berger, Jens Roat Kultima, Luis Pedro Coelho, Manimozhiyan Arumugam, Julien Tap, Henrik Bjørn Nielsen, Simon Rasmussen, Søren Brunak, Oluf Borbye Pedersen, Francisco Guarner, Willem M de Vos, Jun Wang, Junhua Li, Joël Doré, S Dusko Ehrlich, Alexandros StamatakisPeer Bork

Genome Research and Molecular Bio Medicine

253 Citations (Scopus)

Abstract

To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.

Original language	English
Journal	Nature Methods
Volume	10
Issue number	12
Pages (from-to)	1196-1199
Number of pages	4
ISSN	1548-7091
DOIs	https://doi.org/10.1038/nmeth.2693
Publication status	Published - Dec 2013

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Sunagawa, S., Mende, D. R., Zeller, G., Izquierdo-Carrasco, F., Berger, S. A., Kultima, J. R., Coelho, L. P., Arumugam, M., Tap, J., Nielsen, H. B., Rasmussen, S., Brunak, S., Pedersen, O. B., Guarner, F., de Vos, W. M., Wang, J., Li, J., Doré, J., Ehrlich, S. D., ... Bork, P. (2013). Metagenomic species profiling using universal phylogenetic marker genes. Nature Methods, 10(12), 1196-1199. https://doi.org/10.1038/nmeth.2693

Sunagawa, S, Mende, DR, Zeller, G, Izquierdo-Carrasco, F, Berger, SA, Kultima, JR, Coelho, LP, Arumugam, M, Tap, J, Nielsen, HB, Rasmussen, S, Brunak, S, Pedersen, OB, Guarner, F, de Vos, WM, Wang, J, Li, J, Doré, J, Ehrlich, SD, Stamatakis, A & Bork, P 2013, 'Metagenomic species profiling using universal phylogenetic marker genes', Nature Methods, vol. 10, no. 12, pp. 1196-1199. https://doi.org/10.1038/nmeth.2693

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abstract = "To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.",

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T1 - Metagenomic species profiling using universal phylogenetic marker genes

AU - Sunagawa, Shinichi

AU - Mende, Daniel R.

AU - Zeller, Georg

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AU - Berger, Simon A.

AU - Kultima, Jens Roat

AU - Coelho, Luis Pedro

AU - Arumugam, Manimozhiyan

AU - Tap, Julien

AU - Nielsen, Henrik Bjørn

AU - Rasmussen, Simon

AU - Brunak, Søren

AU - Pedersen, Oluf Borbye

AU - Guarner, Francisco

AU - de Vos, Willem M

AU - Wang, Jun

AU - Li, Junhua

AU - Doré, Joël

AU - Ehrlich, S Dusko

AU - Stamatakis, Alexandros

AU - Bork, Peer

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AB - To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.

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DO - 10.1038/nmeth.2693

M3 - Journal article

C2 - 24141494

SN - 1548-7091

VL - 10

SP - 1196

EP - 1199

JO - Nature Methods

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ER -

Metagenomic species profiling using universal phylogenetic marker genes

Abstract

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